Foreword from the Directors

Michael Levine and Ralph
RoskiesPSC co-scientific directors.

Twenty-five years ago, with a grant from the
National Science Foundation, the Pittsburgh Supercomputing Center (PSC) was born. Since then we’ve
participated in breathtaking technological change, and it’s still happening. This year, with partner
sites around the country, we embark on the adventure of XSEDE, the Extreme Science and Discovery
Environment, the most powerful collection of integrated computational resources in the
world.

Two supercomputing systems that we host and make available to the national research
community this year came into productive maturity. With Anton, the world’s most effective system for
simulation of proteins and nucleic acids, computational biologists have opened a new view into
protein dynamics. We briefly describe in this booklet the unique story of Anton and findings from
four of these projects.

Blacklight, the world’s largest shared-memory system,
has rapidly become a force across a
wide and interesting spectrum of fields — including genomics, machine learning, natural language
processing, geophysics and astrophysics.

As a tool for assembly of sequence data from next-generation sequencing tools, Blacklight enabled
remarkably fast results in two projects. One, led by James Vincent, is the sequencing of
an NIH model organism, a fish called the little skate. Similarly, Blacklight accelerated sequence
assembly in the work of Cecilia Lo at the University of Pittsburgh Medical School on congenital
heart defects.

With limitless quantities of text available on World Wide Web, Blacklight’s shared memory is a
powerful tool for sifting words as data — as Noah Smith showed in four papers in diverse fields of
“natural language processing” within six months of access to Blacklight.

For astrophysicists Tiziana Di Matteo and Rupert Croft, Blacklight has revolutionized discovery from
large-scale simulations of how the cosmos evolves. The ability to hold an entire
snapshot of MassiveBlack, their huge simulation, in memory at one time was instrumental in their
ability to reveal “cold gas flows” as a phenomenon that accounts for supermassive black holes in the
early universe.

With help from PSC scientist Marcela Madrid, Catalina Achim solved the structure of a fascinating
molecule called peptide nucleic acid, a close cousin structurally to DNA, but with
important advantages for research in electron transport.

In a major accomplishment, Art Wetzel and Greg Hood, scientists in PSC’s National Resource for
Biomedical Supercomputing, co-authored a paper that appeared as a cover story in
Nature, the prestigious international journal of science. Their collaboration with Clay Reid and
colleagues at Harvard is a milestone in brain research.

Along with these scientific advances, PSC continues to be a resource for research and education in
Pennsylvania. Through the Three Rivers Optical Exchange, PSC’s networking group
serves the Pennsylvania-West Virginia region and carries out nationally recognized research in
next-generation, high-bandwidth Internet resources. This booklet also highlights our
important work to help educate the upcoming generation of scientists and science-literate citizens.

Much more than technology per se, it’s PSC’s staff who make all of this possible. It’s our privilege
to work with a collection of people second-to-none in world-class talent and experience in
high-performance computing. We’re grateful also for support from the National Science Foundation,
the U.S. Department of Energy, the National Institutes of Health, the Commonwealth of Pennsylvania
and many others.